rs7111898

Positions:

• chr11-13187828-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.541 in 151,946 control chromosomes in the GnomAD database, including 23,346 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (23346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82137 AN: 151830 Hom.: 23351 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.564

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.541 AC: 82154 AN: 151946 Hom.: 23346 Cov.: 32 AF XY: 0.532 AC XY: 39506 AN XY: 74266

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.560

Alfa AF: 0.602 Hom.: 12308

Bravo AF: 0.542

Asia WGS AF: 0.394 AC: 1370 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.1
DANN	Benign	0.92

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7111898; hg19: chr11-13209375;